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ONTOLOGY REPORT - ANNOTATIONS

Term:positive regulation of gene expression, epigenetic
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Accession:GO:0141137 term browser browse the term
Definition:An epigenetic process that increases gene expression at specific genomic regions through chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or the cytosine DNA demethylation.
Synonyms:exact_synonym: activation of gene expression, epigenetic;   up regulation of gene expression, epigenetic;   upregulation of gene expression, epigenetic


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positive regulation of gene expression, epigenetic term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Alkbh1 alkB homolog 1, histone H2A dioxygenase involved_in ISO
IEA 		(PMID:30017583), (PMID:30392959)
GO_REF:0000107
(PMID:27027282) 		RGD
Ensembl		 PMID:27027282 PMID:30017583 PMID:30392959 GO_REF:0000107 NCBI chr 6:107,068,301...107,088,784
Ensembl chr 6:107,068,475...107,088,759 		JBrowse link
G Alkbh4 alkB homolog 4, lysine demethylase involved_in ISO
IEA 		(PMID:30982744)
GO_REF:0000107 		RGD
Ensembl		 PMID:30982744 GO_REF:0000107 NCBI chr12:20,524,030...20,529,947
Ensembl chr12:20,524,030...20,529,947 		JBrowse link
G App amyloid beta precursor protein involved_in ISO UniProtKB:P05067-PRO_0000000097|UniProtKB:P05067-PRO_0000000099 (PMID:19057576)
UniProtKB:P05067-PRO_0000000098|UniProtKB:P05067-PRO_0000000099 (PMID:19057576)
UniProtKB:P05067-PRO_0000000097|UniProtKB:P05067-PRO_0000000098 (PMID:19057576) 		RGD PMID:19057576 NCBI chr11:24,019,774...24,236,584
Ensembl chr11:24,019,778...24,236,561 		JBrowse link
chromosomal 5-methylcytosine DNA demethylation, oxidation pathway term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tet1 tet methylcytosine dioxygenase 1 involved_in IEA GO_REF:0000002 InterPro GO_REF:0000002 NCBI chr20:25,761,042...25,840,926
Ensembl chr20:25,768,120...25,833,052 		JBrowse link
G Tet2 tet methylcytosine dioxygenase 2 acts_upstream_of_or_within
involved_in 		ISO
IEA 		MGI:5301343 (PMID:21803851)
GO_REF:0000002 		RGD
InterPro		 PMID:21803851 GO_REF:0000002 NCBI chr 2:221,988,645...222,072,813
Ensembl chr 2:221,988,645...222,072,534 		JBrowse link
G Tet3 tet methylcytosine dioxygenase 3 involved_in IEA GO_REF:0000002 InterPro GO_REF:0000002 NCBI chr 4:115,867,412...115,964,433
Ensembl chr 4:115,871,265...115,964,193 		JBrowse link
negative regulation of transcription initiation-coupled chromatin remodeling term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Kdm1a lysine demethylase 1A involved_in ISO
IEA 		(PMID:33980486)
GO_REF:0000107 		RGD
Ensembl		 PMID:33980486 GO_REF:0000107 NCBI chr 5:148,782,976...148,838,319
Ensembl chr 5:148,782,976...148,838,319 		JBrowse link
G L3mbtl3 L3MBTL histone methyl-lysine binding protein 3 involved_in ISO
IEA 		(PMID:33980486)
GO_REF:0000107 		RGD
Ensembl		 PMID:33980486 GO_REF:0000107 NCBI chr 1:18,988,763...19,089,247
Ensembl chr 1:18,990,618...19,089,263 		JBrowse link
G Samd1 sterile alpha motif domain containing 1 involved_in ISO (PMID:33980486) RGD PMID:33980486 NCBI chr19:24,151,136...24,154,475
Ensembl chr19:24,151,128...24,154,488 		JBrowse link
positive regulation of gene expression via chromosomal CpG island demethylation term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aicda activation-induced cytidine deaminase involved_in ISO (PMID:21496894) RGD PMID:21496894 NCBI chr 4:155,774,132...155,783,972
Ensembl chr 4:155,774,132...155,783,972 		JBrowse link
G Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 involved_in ISS
IEA
ISO 		GO_REF:0000024
GO_REF:0000107
(PMID:21496894) 		UniProt
Ensembl
RGD		 PMID:21496894 GO_REF:0000024 GO_REF:0000107 NCBI chr15:24,144,595...24,146,785
Ensembl chr15:24,144,362...24,146,785 		JBrowse link
G Apobec1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 involved_in ISS
ISO
IEA 		GO_REF:0000024
(PMID:21496894)
GO_REF:0000107 		UniProt
RGD
Ensembl		 PMID:21496894 GO_REF:0000024 GO_REF:0000107 NCBI chr 4:155,800,030...155,828,515
Ensembl chr 4:155,800,887...155,827,390 		JBrowse link
G Apobec2 apolipoprotein B mRNA editing enzyme catalytic subunit 2 involved_in ISO
IEA 		(PMID:21496894)
GO_REF:0000107 		RGD
Ensembl		 PMID:21496894 GO_REF:0000107 NCBI chr 9:12,564,955...12,578,461
Ensembl chr 9:12,564,920...12,578,458 		JBrowse link
G Egr1 early growth response 1 involved_in IEA
ISO 		GO_REF:0000107
UniProtKB:Q3URK3 (PMID:31467272) 		Ensembl
RGD		 PMID:31467272 GO_REF:0000107 NCBI chr18:26,737,078...26,740,877
Ensembl chr18:26,462,981...26,466,766 		JBrowse link
G Ftx FTX transcript, XIST regulator acts_upstream_of_or_within ISO (PMID:21118898) RGD PMID:21118898 NCBI chr  X:68,588,349...68,630,338 JBrowse link
G Ogg1 8-oxoguanine DNA glycosylase involved_in ISO (PMID:27251462) RGD PMID:27251462 NCBI chr 4:146,474,701...146,481,959
Ensembl chr 4:146,474,750...146,484,766 		JBrowse link
G Tet1 tet methylcytosine dioxygenase 1 involved_in
acts_upstream_of_or_within 		ISO (PMID:21496894)
UniProtKB:P08046 (PMID:19372391), (PMID:21496894), (PMID:31467272)
MGI:4129024 (PMID:20639862), (PMID:21295276), (PMID:24291790) 		RGD PMID:19372391 PMID:20639862 PMID:21295276 PMID:21496894 PMID:24291790 More... NCBI chr20:25,761,042...25,840,926
Ensembl chr20:25,768,120...25,833,052 		JBrowse link
G Tet2 tet methylcytosine dioxygenase 2 involved_in
acts_upstream_of_or_within 		ISO (PMID:24315485)
(PMID:20639862) 		RGD PMID:20639862 PMID:24315485 NCBI chr 2:221,988,645...222,072,813
Ensembl chr 2:221,988,645...222,072,534 		JBrowse link
G Tet3 tet methylcytosine dioxygenase 3 acts_upstream_of_or_within ISO
IEA 		(PMID:20639862)
GO_REF:0000107 		RGD
Ensembl		 PMID:20639862 GO_REF:0000107 NCBI chr 4:115,867,412...115,964,433
Ensembl chr 4:115,871,265...115,964,193 		JBrowse link
G Zmpste24 zinc metallopeptidase STE24 acts_upstream_of_or_within ISO
IEA 		MGI:2180033 (PMID:20961378)
GO_REF:0000107 		RGD
Ensembl		 PMID:20961378 GO_REF:0000107 NCBI chr 5:134,627,218...134,660,360
Ensembl chr 5:134,627,229...134,660,110 		JBrowse link
transcription initiation-coupled chromatin remodeling term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ash2l ASH2 like histone lysine methyltransferase complex subunit involved_in ISO (PMID:19556245) RGD PMID:19556245 NCBI chr16:66,242,205...66,264,064
Ensembl chr16:66,242,212...66,264,061 		JBrowse link
G Atad2 ATPase family, AAA domain containing 2 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 7:89,634,123...89,676,738
Ensembl chr 7:89,634,123...89,676,738 		JBrowse link
G Atad2b ATPase family, AAA domain containing 2B involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 6:27,914,546...28,070,103
Ensembl chr 6:27,912,862...28,067,047 		JBrowse link
G Atf2 activating transcription factor 2 involved_in ISO (PMID:10821277) RGD PMID:10821277 NCBI chr 3:79,125,814...79,202,896
Ensembl chr 3:58,718,332...58,795,236 		JBrowse link
G Bckdk branched chain ketoacid dehydrogenase kinase involved_in IEA GO_REF:0000107 Ensembl GO_REF:0000107 NCBI chr 1:191,945,809...191,950,480
Ensembl chr 1:182,515,327...182,536,633 		JBrowse link
G Brd7 bromodomain containing 7 involved_in ISO
IEA 		(PMID:20228809)
GO_REF:0000107 		RGD
Ensembl		 PMID:20228809 GO_REF:0000107 NCBI chr19:18,708,792...18,737,497
Ensembl chr19:18,709,022...18,737,494 		JBrowse link
G Ctcfl1 CCCTC-binding factor like 1 involved_in ISO
IEA 		(PMID:18765639)
GO_REF:0000107 		RGD
Ensembl		 PMID:18765639 GO_REF:0000107 NCBI chr 3:161,868,306...161,890,949
Ensembl chr 3:161,868,306...161,890,949 		JBrowse link
G Dpy30 dpy-30 histone methyltransferase complex regulatory subunit involved_in ISS
ISO 		GO_REF:0000024
(PMID:19556245) 		UniProt
RGD		 PMID:19556245 GO_REF:0000024 NCBI chr 6:21,120,947...21,141,720
Ensembl chr 6:21,120,947...21,141,432 		JBrowse link
G Ep300 E1A binding protein p300 involved_in ISO (PMID:25818647), (PMID:27256286) RGD PMID:25818647 PMID:27256286 NCBI chr 7:114,987,857...115,058,652
Ensembl chr 7:113,106,247...113,136,088
Ensembl chr 7:113,106,247...113,136,088 		JBrowse link
G Fam47a family with sequence similarity 47, member A involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr  X:42,762,231...42,763,887
Ensembl chr  X:42,762,229...42,763,883 		JBrowse link
G Fam47e family with sequence similarity 47, member E involved_in ISO
IEA 		(PMID:33376131)
GO_REF:0000107 		RGD
Ensembl		 PMID:33376131 GO_REF:0000107 NCBI chr14:15,485,537...15,521,599
Ensembl chr14:15,485,127...15,521,775 		JBrowse link
G Glyr1 glyoxylate reductase 1 homolog involved_in ISO
IEA 		(PMID:30970244)
GO_REF:0000107 		RGD
Ensembl		 PMID:30970244 GO_REF:0000107 NCBI chr10:10,532,036...10,567,639
Ensembl chr10:10,532,154...10,567,637 		JBrowse link
G Kat7 lysine acetyltransferase 7 involved_in ISO
IEA 		(PMID:21856198)
GO_REF:0000107
(PMID:21149574) 		RGD
Ensembl		 PMID:21149574 PMID:21856198 GO_REF:0000107 NCBI chr10:80,718,335...80,752,387
Ensembl chr10:80,221,524...80,255,567 		JBrowse link
G Kat8 lysine acetyltransferase 8 involved_in IEA
ISO 		GO_REF:0000107
(PMID:15960975) 		Ensembl
RGD		 PMID:15960975 GO_REF:0000107 NCBI chr 1:191,954,827...191,967,107
Ensembl chr 1:182,515,327...182,536,633 		JBrowse link
G Kdm1b lysine demethylase 1B involved_in ISO (PMID:30970244) RGD PMID:30970244 NCBI chr17:17,602,961...17,643,865
Ensembl chr17:17,602,961...17,643,800 		JBrowse link
G Kdm2a lysine demethylase 2A involved_in ISO (PMID:32584788) RGD PMID:32584788 NCBI chr 1:201,612,427...201,682,359
Ensembl chr 1:201,612,453...201,680,787 		JBrowse link
G Kmt2a lysine methyltransferase 2A involved_in ISO
IEA 		(PMID:15960975), (PMID:19556245)
GO_REF:0000107 		RGD
Ensembl		 PMID:15960975 PMID:19556245 GO_REF:0000107 NCBI chr 8:45,116,763...45,193,320
Ensembl chr 8:45,118,814...45,193,181 		JBrowse link
G Lcor ligand dependent nuclear receptor corepressor involved_in ISO (PMID:29628311) RGD PMID:29628311 NCBI chr 1:240,298,565...240,405,627
Ensembl chr 1:240,298,563...240,402,448 		JBrowse link
G Letmd1 LETM1 domain containing 1 acts_upstream_of_or_within ISO (PMID:34910916) RGD PMID:34910916 NCBI chr 7:131,584,241...131,597,797
Ensembl chr 7:131,584,259...131,597,796 		JBrowse link
G LOC102552474 protein FAM47E-like involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr  X:13,775,705...13,777,481
Ensembl chr  X:13,776,114...13,777,409 		JBrowse link
G Macroh2a1 macroH2A.1 histone involved_in ISO
IEA 		(PMID:25526730)
GO_REF:0000107 		RGD
Ensembl		 PMID:25526730 GO_REF:0000107 NCBI chr17:8,479,331...8,542,071
Ensembl chr17:8,479,372...8,542,072 		JBrowse link
G Men1 menin 1 involved_in ISO
IEA 		(PMID:14992727)
GO_REF:0000107 		RGD
Ensembl		 PMID:14992727 GO_REF:0000107 NCBI chr 1:213,068,166...213,074,132
Ensembl chr 1:203,639,000...203,644,871 		JBrowse link
G Myocd myocardin involved_in ISS
ISO 		GO_REF:0000024
(PMID:15601857) 		UniProt
RGD		 PMID:15601857 GO_REF:0000024 NCBI chr10:49,833,219...49,928,806
Ensembl chr10:49,836,641...49,927,627 		JBrowse link
G N6amt1 N-6 adenine-specific DNA methyltransferase 1 involved_in ISO (PMID:31061526) RGD PMID:31061526 NCBI chr11:26,584,750...26,597,790
Ensembl chr11:26,584,724...26,608,248 		JBrowse link
G Noc2l NOC2-like nucleolar associated transcriptional repressor involved_in ISO
IEA 		(PMID:16322561)
GO_REF:0000107 		RGD
Ensembl		 PMID:16322561 GO_REF:0000107 NCBI chr 5:166,820,150...166,831,949
Ensembl chr 5:166,820,161...166,831,949 		JBrowse link
G Nr3c1 nuclear receptor subfamily 3, group C, member 1 involved_in IMP PMID:12917342 UniProt PMID:12917342 RGD:8553888 NCBI chr18:31,522,783...31,644,508
Ensembl chr18:31,271,681...31,393,375 		JBrowse link
G Pabpc1l poly(A) binding protein, cytoplasmic 1-like acts_upstream_of_or_within ISO
IEA 		MGI:5437740 (PMID:26134869)
GO_REF:0000107 		RGD
Ensembl		 PMID:26134869 GO_REF:0000107 NCBI chr 3:152,692,825...152,725,997
Ensembl chr 3:152,693,700...152,725,997 		JBrowse link
G Padi2 peptidyl arginine deiminase 2 involved_in ISO (PMID:22853951) RGD PMID:22853951 NCBI chr 5:153,209,053...153,251,632
Ensembl chr 5:153,209,053...153,251,632 		JBrowse link
G Phf2 PHD finger protein 2 involved_in ISO
IEA 		(PMID:22921934)
GO_REF:0000107 		RGD
Ensembl		 PMID:22921934 GO_REF:0000107 NCBI chr17:15,783,221...15,851,209
Ensembl chr17:15,781,864...15,851,208 		JBrowse link
G Prmt3 protein arginine methyltransferase 3 involved_in ISO (PMID:31378783) RGD PMID:31378783 NCBI chr 1:99,492,712...99,581,774
Ensembl chr 1:99,492,724...99,579,435 		JBrowse link
G Rbbp5 RB binding protein 5, histone lysine methyltransferase complex subunit involved_in ISO
IEA 		(PMID:19556245)
GO_REF:0000107 		RGD
Ensembl		 PMID:19556245 GO_REF:0000107 NCBI chr13:43,912,254...43,939,107
Ensembl chr13:43,912,254...43,939,107 		JBrowse link
G Rbm14 RNA binding motif protein 14 involved_in ISO
IEA 		UniProtKB:Q92793 (PMID:11443112)
GO_REF:0000107 		RGD
Ensembl		 PMID:11443112 GO_REF:0000107 NCBI chr 1:202,076,940...202,105,688
Ensembl chr 1:202,078,287...202,105,665
Ensembl chr 1:202,078,287...202,105,665 		JBrowse link
G Sgf29 SAGA complex associated factor 29 involved_in ISO
ISS 		(PMID:23894581)
GO_REF:0000024 		RGD
UniProt		 PMID:23894581 GO_REF:0000024 NCBI chr 1:181,238,458...181,271,931
Ensembl chr 1:181,238,468...181,274,781 		JBrowse link
G Sirt7 sirtuin 7 involved_in ISO (PMID:28655758) RGD PMID:28655758 NCBI chr10:106,394,802...106,401,627
Ensembl chr10:105,896,476...105,903,172 		JBrowse link
G Smarca4 SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 involved_in ISO (PMID:34910916) RGD PMID:34910916 NCBI chr 8:28,438,370...28,535,071
Ensembl chr 8:20,167,717...20,258,975 		JBrowse link
G Smarcb1 SWI/SNF related BAF chromatin remodeling complex subunit B1 involved_in ISO (PMID:22368283) RGD PMID:22368283 NCBI chr20:12,741,164...12,763,616
Ensembl chr20:12,741,477...12,763,620 		JBrowse link
G Smarcd1 SWI/SNF related BAF chromatin remodeling complex subunit D1 involved_in ISO
IEA 		(PMID:12917342)
GO_REF:0000107 		RGD
Ensembl		 PMID:12917342 GO_REF:0000107 NCBI chr 7:130,829,783...130,840,323
Ensembl chr 7:130,829,768...130,840,323 		JBrowse link
G Sphk2 sphingosine kinase 2 involved_in ISO
IEA 		(PMID:19729656)
GO_REF:0000107 		RGD
Ensembl		 PMID:19729656 GO_REF:0000107 NCBI chr 1:96,180,872...96,188,592
Ensembl chr 1:96,180,887...96,188,391 		JBrowse link
G Spi1 Spi-1 proto-oncogene involved_in ISO
IEA
ISS 		(PMID:33951726)
GO_REF:0000107
(PMID:30171019)
GO_REF:0000024 		RGD
Ensembl
UniProt		 PMID:30171019 PMID:33951726 GO_REF:0000024 GO_REF:0000107 NCBI chr 3:77,059,744...77,093,730
Ensembl chr 3:77,073,012...77,092,393 		JBrowse link
G Tp53 tumor protein p53 involved_in ISO
IEA 		(PMID:16322561)
GO_REF:0000107 		RGD
Ensembl		 PMID:16322561 GO_REF:0000107 NCBI chr10:54,798,871...54,810,300
Ensembl chr10:54,300,048...54,311,524 		JBrowse link
G Trmt112 tRNA methyltransferase activator subunit 11-2 involved_in ISO (PMID:31061526) RGD PMID:31061526 NCBI chr 1:204,103,298...204,104,151 JBrowse link
G Usp21 ubiquitin specific peptidase 21 involved_in ISS
ISO 		GO_REF:0000024
(PMID:18172164) 		UniProt
RGD		 PMID:18172164 GO_REF:0000024 NCBI chr13:83,702,672...83,709,215
Ensembl chr13:83,702,631...83,708,717 		JBrowse link
G Vps72 vacuolar protein sorting 72 homolog involved_in ISO
IEA 		UniProtKB:P06899|UniProtKB:P0C0S5 (PMID:26974126)
GO_REF:0000107 		RGD
Ensembl		 PMID:26974126 GO_REF:0000107 NCBI chr 2:182,678,594...182,690,185
Ensembl chr 2:182,678,609...182,690,182 		JBrowse link
G Wbp2 WW domain binding protein 2 involved_in ISO
IEA 		(PMID:23233354)
GO_REF:0000107 		RGD
Ensembl		 PMID:23233354 GO_REF:0000107 NCBI chr10:101,312,476...101,320,775
Ensembl chr10:101,312,446...101,320,736 		JBrowse link
G Wdr5 WD repeat domain 5 involved_in ISS
ISO 		GO_REF:0000024
(PMID:19556245) 		UniProt
RGD		 PMID:19556245 GO_REF:0000024 NCBI chr 3:10,836,964...10,856,682
Ensembl chr 3:10,837,025...10,856,671 		JBrowse link
G Znhit1 zinc finger, HIT-type containing 1 involved_in ISO
IEA 		(PMID:30842416), (PMID:35167494)
GO_REF:0000107 		RGD
Ensembl		 PMID:30842416 PMID:35167494 GO_REF:0000107 NCBI chr12:19,686,606...19,692,880
Ensembl chr12:19,686,148...19,692,880 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 20543
    cellular process 19534
      metabolic process 12158
        biosynthetic process 8630
          macromolecule biosynthetic process 7628
            gene expression 7191
              positive regulation of gene expression 1362
                positive regulation of gene expression, epigenetic 63
                  chromosomal 5-methylcytosine DNA demethylation, oxidation pathway 3
                  transcription initiation-coupled chromatin remodeling + 60
Path 2
Term Annotations click to browse term
  biological_process 20543
    biological regulation 13835
      regulation of biological process 13398
        regulation of cellular process 13032
          regulation of metabolic process 6776
            regulation of biosynthetic process 5581
              regulation of macromolecule biosynthetic process 5373
                regulation of gene expression 5256
                  positive regulation of gene expression 1362
                    positive regulation of gene expression, epigenetic 63
                      chromosomal 5-methylcytosine DNA demethylation, oxidation pathway 3
                      transcription initiation-coupled chromatin remodeling + 60
paths to the root